Bioinformatics support for the Baker Institute: team and projects update

Domain Bioinformatics

Sergio Ruiz Carmona, Artika Nath and Rodrigo Canovas September 2021

Provide Support Role for all Baker Laboratories

Started

2017

-Project work

-Grant applications -Consultations

2021

3 Bioinformaticians

35 projects – completed

Data analysis

5 grant applications

4 manuscripts published

17 projects – ongoing

5 manuscripts in preparation

1 manuscript submitted

Major underpinning ANALYTICS infrastructure for Baker

MISSION: To build bioinformatics capacity at the Baker Institute through collaboration, support and training

CAPABILITES: Analysis of data and cross-omic integration from diverse technologies:

Genomics

Epigenomics

Transcriptomics (Bulk & single cell)

Proteomics

Metabolomics

Metagenomics

Blood cell traits

APPROACHES:

Statistical analysis

Machine learning

Network analysis

High dimensional data normalisation, processing & visualisation

Design of computational algorithms

Who we are

Artika Nath

PhD in Bioinformatics (University Of Melbourne)

Integrative genomics

Functional analysis

Network/Cluster analysis

Data & Statistical Analysis

Gene expression analysis (Bulk & Single Cell)

GWAS (Univariate & Multivariate)

eQTL and Colocalisation Analysis

Postdoctoral Researcher / Bioinformatician (Baker)

Since 2018

Integrative genomics

Data science, manipulation, visualisation

Analysis of transcriptomics, metabolomics, protein data

UK-Biobank Related projects

Cambridge Baker Systems Genomics Initiative

Co-Lead on the INTERVAL RNA-Seq project

5000 samples with RNA-seq data

eQTL analysis, colocalisation analysis, coexpression network analysis, Integration with other molecular traits

Nath et al., 2019

Nath et al., 2017

Nath et al., 2019

Nath et al., 2019

Investigate the transcriptomic profile of reduced cardiac O-GlcNAcylation in the diabetic heart

Excessive O-GlcNAcylation is suspected to contribute to myocardial dysfunction in diabetes

The global transcriptomic profile of

Collaboration - Darnel Prakoso

 

Prof. Rebecca Ritchie’s Lab

 

OGA-treated diabetic mice is similar

 

 

 

 

 

 

to non-diabetic mice

 

 

 

 

Non-Diabetic

 

 

 

 

 

 

 

 

Diabetic

Diabetic - OGA

OGA - reduces O-GlcNAcylation

 

 

 

Enrichment analysis revealed that

 

 

 

OGA administration altered pathway

 

 

 

associated with cardiac remodelling.

Fffffffffffffffi

 

i

 

 

Prakoso, Nath, et al - Manuscript in Prep.

Rodrigo Cánovas

PhD - Engineering, The University of Melbourne, Australia

In the disciplines of Bioinformatics Software and Coding and Information Theory

Finished in 2015

Practical Compression for Multi-Alignment Genomic Files

Postdoctoral Researcher, LIRMM and IBC, France

From 2015 to end of 2017

Developing algorithms for analysing next-generation sequencing data

Research Officer / Bioinformatician, Baker Institute, Australia

Since 2018, Systems Genomics lab

Genomic risk prediction

Data science, manipulation and visualization

Bioinformatics and Computer Science including, between others:

Genomic risk prediction, survival analysis, design and analysis of algorithms and data structures, indexing, compression, pattern matching , machine learning, deep learning, data analysis

COVID-19 and venous thromboembolism disease (VTE) association

(Status: manuscript of exploratory analysis )

Among UK Biobank participants who were COVID-19 tested we are exploring the following research questions:

I.Does the predictors of genetic predisposition for VTE helps to predict the development of COVID-19?

II. Considering only individuals that tested positive. Are predictors of genetic predisposition for VTE associated with an increase in the mortality rate from COVID-19?

III. Association of COVID-19 with developing VTE disease

Collaboration with Baker’s Atherothrombosis and

Vascular Biology Lab:

Hannah Stevens

Dr James McFadyen

Parameters Correlation plot

Predicting Covid-Status

RDH11 target role in humans

Collaboration with Baker’s Lipid Metabolism and

Cardiometabolic Disease Lab:

Dr Michael Keating

Among the UK Biobank:

I.Understand what role that RDH11 might be playing in humans

II.Check if RDH11 is associated with phenotypes linked to these pathways A. (eg. phenotypes associated with variation at the RDH11 locus)

Sergio Ruiz Carmona

PhD in Computational Biology and Drug Discovery

Finished in 2017 in Barcelona (Spain)

Method development and applications in drug design

Postdoc in drug discovery for blood disorders

In Barcelona (Spain)

Drug patent & spin-off to progress into clinical trials

EMBO short-term fellow in Pharmacogenomics

Research Officer / Bioinformatician @Baker Institute

Since early 2019, Systems Genomics lab

Protein structure genomics

Data science, manipulation and visualization

Bioinformatics and gene expression analysis

Machine learning and High Performance Computing

UK Biobank

Web development and interactive applications / dashboards

Oxygen Pathway analysis in CTEPH patients

Collaboration with the

Sports Cardiology Lab

Dr. Erin Howden

Dr. Guido Claessen

A/Prof Andre La Gerche

Interactive

Shiny App

Baker quarterly publication award (presentation next Tuesday, 7th)

lncRNAs in physiological and pathological hypertrophy

Collaboration with the

Cardiac Hypertrophy Lab

Dr. Jenny Ooi

Prof. Julie McMullen

TrainingPeaks - Athlete data analysis

~200 athletes

60.000 training activities

Collaboration with the

Sports Cardiology Lab

Kristel Janssens

Dr. Guido Claessen

A/Prof Andre La Gerche

How does it work?

How can Baker researchers engage with us?

How does the process look like?

What can you expect from us?

How much is it?

We work with a collaborative model

-Authorship in papers

-Grant participation

-General advice

Project requests

https://intranet.baker.edu.au/resear ch-resources/platform-

technologies/bioinformatics- program/domain-bioinformatics/

Search

Domain Bioinformatics

on the intranet search box

Research resources >

Platform Technologies >

Bioinformatics Program >

Domain Bioinformatics

Request & project timeline

First email

Initial

Initial

Meeting

analysis &

request

(Full team)

report

 

Updated

Follow-up

analysis &

Meetings

report

 

Ideal situation

Background

Ideal

information

Outcome

Data

analysis

Also...

UK Biobank Projects

Recruited Individuals

Recruited ~500,000 UK individuals (not families) between 2006 – 2010

Image obtained from the UKB webpage

UK Biobank Timeline

Covid-19

DataNightingale Health’s study

Blood samples

120,000

20202021

Exome

sequencing of

200,000

Image adapted from R. Collins UKB slides

Principles of accessing UK Biobank

Open access resource, available for bona fide researchers to conduct health-related research that is in the public interest

Researchers are obliged to return their results to UK Biobank so they can be shared with others

Any work/presentation/publication must include the following phrase:

“This research has been conducted using the UK Biobank Resource under application number 55469”

Using the Baker-wide UKB project #55469

Access the UK Biobank

Register with the UK Biobank

https://www.ukbiobank.ac.uk/enable-your-research/register

Contact Mike Inouye or Domain Bioinformatician Team to:

Be added to Baker’s approved UKB project

Rules of how to use the UKB data:

If you have data science training specific arrangements can be made to grant access to the data

All UKB data must be and remain on the server (common Baker cluster)

NO UKB DATA IS TO BE TRANSFERRED OFF THE SERVER

Using the Baker-wide UKB project #55469

Suggested Project Pipeline:

Request access to the UKB

Explore what have been done already

Submit a project request to the Domain Bioinformatics group

Before the first meeting check on the UKB showcase which data would be useful

Some links that may help:

Create some amazing research

Report results back to the UK Biobank

Thank you!

bioinformatics@baker.edu.au

Domain Bioinformatics

Sergio Ruiz Carmona, Artika Nath and Rodrigo Canovas September 2021